Microsoft Intune supports the deployment of applications using InstallApplication. This opens the possibility to manage Mac computers with Microsoft Intune, and automatically push Munki to provide additional functionality.

As far as I know, there’s no way to make these macOS LOB apps to be installed during the setup assistant (also called: “Bootstrap package”. In practice, the delay between enrolment and the app being deployed can be quite long (I’ve seen 5 minutes while clicking on “Sync” frantically). Also, Microsoft Intune seem to be a little slow to report success or failure in the console. Perhaps time for a User voice feedback?